Searching journal content for articles similar to Coey and Clark 32 (2): 367.

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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...factor-specific antibodies; the exact mechanisms of the interplay of all TFs and nucleosomes have yet to be explored with respect to transcription.To address these challenges, here we develop a systematic, genetic approach to simultaneously profile nucleosome and TF changes in response to single...
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Research: Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A
- Neelam Dabas Sen,
- Fujun Zhou,
- Nicholas T. Ingolia,
- and Alan G. Hinnebusch
Genome Res. August 2015 25: 1196-1205; Published in Advance June 29, 2015, doi:10.1101/gr.191601.115
...genes and -average length (79 nt) are shown. (B) Schematic showing 5′ UTR intervals assigned for calculating cumulative PARS scores. (C) Average PARS scores calculated for the indicated gene set for each 5′ UTR interval described in B. (*) P < 0.05. (D) Genome-wide changes in TE are negatively...
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Research: A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs
- Yue Yun,
- T.M. Ayodele Adesanya,
- and Robi D. Mitra
Genome Res. June 2012 22: 1089-1097; Published in Advance March 27, 2012, doi:10.1101/gr.117366.110
...and molecular mechanisms underlying this class of mutations. A genome-wide analysis showed that genes with uAUGs display significantly lower mRNA and protein levels than genes without uAUGs. To determine the generality of this mechanism, we introduced uAUGs into S. cerevisiae genes and observed significantly...
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Methods: Distinguishing direct versus indirect transcription factor–DNA interactions
- Raluca Gordân,
- Alexander J. Hartemink,
- and Martha L. Bulyk
Genome Res. November 2009 19: 2090-2100; Published in Advance August 3, 2009, doi:10.1101/gr.094144.109
...-derivedmotifs in the ChIP-chip data set Gcn4_SM. Themotif of Gcn4 (the factor profiled in that ChIP-chip experiment) is the most highly enriched, with the second ranked motif having a significantly lower AUC value. Furthermore, the only significantly enrichedmotif (P-value# 0.001) is that of Gcn4. Thus, in this case we...
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Methods: Incorporating nucleosomes into thermodynamic models of transcription regulation
- Tali Raveh-Sadka,
- Michal Levo,
- and Eran Segal
Genome Res. August 2009 19: 1480-1496; Published in Advance May 18, 2009, doi:10.1101/gr.088260.108
...to generalize from the behavior seen in this promoter to predicted behaviors in other promoters. In the remaining sections, we perform a more systematic exploration of the role of nucleosomes in transcription by focusing on more abstract promoters that code for much simpler affinity landscapes for nucleosome...
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LETTER: Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation
- Moshe Pritsker,
- Yir-Chung Liu,
- Michael A. Beer,
- and Saeed Tavazoie
Genome Res. January 2004 14: 99-108; Published in Advance December 12, 2003, doi:10.1101/gr.1739204
.... Specificity, free energy and information content in protein-DNA interactions. Trends Biochem. Sci. 23 : 109 -113. ↵ Sudarsanam, P., Pilpel, Y., and Church, G.M. 2002 . Genome-wide co-occurrence of promoter elements reveals a cis -regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae...
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METHODS: Candidate Regulatory Sequence Elements for Cell Cycle-Dependent Transcription in Saccharomyces cerevisiae
- Tyra G. Wolfsberg,
- Andrei E. Gabrielian,
- Michael J. Campbell,
- Raymond J. Cho,
- John L. Spouge,
- and David Landsman
Genome Res. August 1, 1999 9: 775-792; doi:10.1101/gr.9.8.775
...of Medicine, Stanford, California 94305 USA Abstract Recent developments in genome-wide transcript monitoring have led to a rapid accumulation of data from gene expression studies. Such projects highlight the need for methods to predict the molecular basis of transcriptional coregulation...
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Perspective: Ribosome decision graphs for the representation of eukaryotic RNA translation complexity
- Jack A.S. Tierney,
- Michał Świrski,
- Håkon Tjeldnes,
- Jonathan M. Mudge,
- Joanna Kufel,
- Nicola Whiffin,
- Eivind Valen,
- and Pavel V. Baranov
Genome Res. April 2024 34: 530-538; Published in Advance May 7, 2024, doi:10.1101/gr.278810.123
...and Wek 2012; Andreev et al. 2023), which protects translation of certain mRNAs (e.g., human ATF4, yeast GCN4) from down-regulation during the integrated stress response (ISR) (Pakos-Zebrucka et al. 2016; Costa-Mattioli and Walter 2020). Under this condition, the reduced availability of the ternary...
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Method: Probing the effect of promoters on noise in gene expression using thousands of designed sequences
- Eilon Sharon,
- David van Dijk,
- Yael Kalma,
- Leeat Keren,
- Ohad Manor,
- Zohar Yakhini,
- and Eran Segal
Genome Res. October 2014 24: 1698-1706; Published in Advance July 16, 2014, doi:10.1101/gr.168773.113
...-disfavoring sequences are an efficient tool for increasing expression while maintaining low noise. To examine the effect of varying the number and configuration of transcription activator binding sites on noise, we examined a set of 643 promoters that contains 0–7 Gcn4 binding sites in various positions and background...
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Research: Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination
- Josefina Ocampo,
- Răzvan V. Chereji,
- Peter R. Eriksson,
- and David J. Clark
Genome Res. March 2019 29: 407-417; Published in Advance January 25, 2019, doi:10.1101/gr.242032.118
...on the coding regions of Gcn4-dependent genes extends into neighbouring genes. Nucleic Acids Res 39: 9521–9535. doi:10.1093/nar/gkr643 ↵Cole HA, Howard BH, Clark DJ. 2012. Genome-wide mapping of nucleosomes in yeast using paired-end sequencing. Meth Enzymol 513: 145–168. doi:10.1016/B978...

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